• The Korean Journal of Blood Transfusion
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• v.29 no.3
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• pp.310-319
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• 2018

Background: Research on next-generation sequencing (NGS)-based HLA typing is active. To resolve the phase ambiguity and long turn-around-time of conventional high resolution HLA typing, this study developed a NGS-based high resolution HLA typing method that can handle large-scale samples within an efficient testing time. Methods: For HLA NGS, the condition of nucleic acid extraction, library construction, PCR mechanism, and HLA typing with bioinformatics were developed. To confirm the accuracy of the NGS-based HLA typing method, the results of 192 samples HLA typed by SSOP and 28 samples typed by SBT compared to NGS-based HLA-A, -B and -DR typing. Results: DNA library construction through two-step PCR, NGS sequencing with MiSeq (Illumina Inc., San Diego, USA), and the data analysis platform were established. NGS-based HLA typing results were compatible with known HLA types from 220 blood samples. Conclusion: The NSG-based HLA typing method could handle large volume samples with high-throughput. Therefore, it would be useful for HLA typing of bone marrow donation volunteers.

• Pediatric Infection and Vaccine
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• v.29 no.1
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• pp.54-60
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• 2022

Salmonella meningitis is rare yet poses causes significant neurological morbidity in children. Infants, especially those under 3 months of age, and those with immunocompromised states, such as malignancy, malaria, and human immunodeficiency virus infection, are at increased risk for developing Salmonella meningitis. Herein, we describe a case of Salmonella meningitis in a previous healthy 8-year-old girl who presented with high fever, vomiting, and altered mental status. Group D Salmonella species were isolated in cerebrospinal fluid culture, and no abnormal findings were noted in brain magnetic resonance imaging. Immunoglobulin levels and lymphocyte subset counts were within the normal ranges, and no genetic mutation responsible for primary immunodeficiency disease was detected by next-generation sequencing. The patient's condition improved rapidly with third-generation cephalosporin, and no complications or sequalae developed. Nontyphoidal Salmonella can cause meningitis in immunocompetent children and can be successfully treated with early administration of antibiotics.

• Proceedings of KOSOMES biannual meeting
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• 2017.11a
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• pp.209-209
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• 2017

• The Korean Journal of Mycology
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• v.46 no.1
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• pp.69-74
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• 2018

The Rhododendron powdery mildew fungus Erysiphe izuensis has been recorded throughout Asia, including China, Japan, Korea, and Russia. In Korea, E. izuensis has been identified based on morphological characteristics of the anamorph found on introduced Rhododendron spp. We here describe the first identification of E. izuensis collected from Rhododendron yedoense f. poukhanense in Korea. Morphological characteristics of the teleomorph as well as internal transcribed spacer sequences of the species are provided. Moreover, we describe the characteristics of the primary conidia and conidial surface pattern of E. izuensis for the first time.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.64-64
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• 2018

생물전환(Bioconversion)은 천연소재의 기능성을 증대시키기 위한 방안으로 많은 연구가 진행되고 있으며 다양한 산업에서도 활용되고 있어 유용미생물을 기반 차세대 기술로 각광받고 있다. 이러한 기술의 도입은 식품은 물론 의약품 및 화장품 산업에서도 활발히 사용되고 있으며, 특히 최근 기능성 제품에 대한 소비가 급증함에 따라 그 중요성이 높아지고 있다. 산초(Zanthoxylum schinfolium)는 limonene, citronellal, phellandrene 등의 다양한 유효물질을 함유하고 있으며 유효성분들로부터 유래되는 항산화 활성과 항암활성, 항균활성 등의 효능을 지니는 것으로 보고된바 있다. 본 연구의 생물전환 공정에 사용된 유산균들은 전통 발효식품으로 알려진 다양한 젓갈류로부터 분리하였으며, 16S rDNA 염기서열 분석을 통해 유전학적 특성을 확인하였다. 또한 확보된 유산균들을 사용하여 산초(전북 진안군) 분말의 발효공정을 수행하였으며, 산초의 최적 추출조건을 선정하고 추출물을 제조하여 생물전환 공정 전 후 활성의 변화추이를 관찰하였다. 추출물의 활성평가는 항산화 효능 및 유효성분 함량을 평가하기 위하여 DPPH radical scavenging activity와 total polyphenol 함량을 평가하고 세포주를 활용해 MTT assay, Nitric oxide(NO) 생성억제 효능을 확인하여 세포독성 및 항염증 활성을 확인하였다. 실험결과, 생물전환 공정에 사용할 유용 미생물을 확보하기 위한 실험을 통해 다양한 젓갈류에서 다양한 미생물을 확보할 수 있었으며 약 16종의 유산균을 분리하였다. 분리된 미생물을 사용하여 산초 분말의 생물전환 공정을 실시한 결과, 5종의 유용미생물 처리에서 무처리 대비 DPPH radical 소거능 및 polyphenol 함량이 유의적으로 증가됨을 확인할 수 있었다. 그 중 가장 높은 활성을 나타내는 균주를 16S rDNA 염기서열 분석을 통해 확인한 결과 Weissella confusa D1로 확인되었다. 선별 균주를 활용한 생물전환 공정 후 항산화 활성은 대조군 대비 약 120%의 활성을 나타냈으며, polyphenol의 함량은 약 126%로 증가하는 것을 확인할 수 있었다. 더 나아가 생물전환 공정 후 산초추출물의 세포독성은 처리전과 비교하여 월등히 감소하는 경향을 확인할 수 있었으며, 항염효능 또한 증가하는 경향을 나타내는 것이 확인되었다.

• Korean Journal of Microbiology
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• v.52 no.2
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• pp.175-182
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• 2016

In this study, we isolated aromatic compounds (lignin polymers) utilizing bacteria in humus layer of oak forest and investigated phylogenetic characteristics and correlation with major bacterial populations in the humus layer by pyrosequencing. Forty-two isolates using aromatic compounds such as p-anisic acid, benzoic acid, ferulic acid and p-coumaric acid were isolated and phylogentic analyses based on 16S rRNA gene sequences showed that the isolates belonged to the genus Rhizobium, Sphingomonas, Burkhorlderia, and Pseudomonas. Among these, Burkhorlderia species which belong to Betaproteobacteria class occupied 83% among the isolates. The bacterial populations in humus layer of oak forest were characterized by next generation pyrosequencing based on 16S rRNA gene sequences. The humus sample produced 7,862 reads, 1,821 OTUs and 6.76 variability index with 97% of significance level, respectively. Bacterial populations consist of 22 phyla and Betaproteobacteria were the major phylum consisting of 15 genera including Burkholderia, Polaromonas, Ralstoria, Zoogloea, and Variovorax. Approximately fifty percentage of them was Burkholderia. Burkholderia as the majority of population in the humus was considered to play a role in degrading lignin in humus layer of oak forest.

• Journal of Korean Society of Forest Science
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• v.106 no.2
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• pp.121-129
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• 2017

The soil microbiome plays important roles in material cycling and plant growth in forest ecosystem. Although a lot of researches on forest soil fungi in Korea have been performed, the studies on forest soil bacterial communities have been limited. In this study, we conducted next generation sequencing (NGS) targeting 16S rRNA gene to investigate the soil bacterial communities from natural red pine (Pinus densiflora) forest in Mt. Janggunbong, Bonghwa-gun, Gyeongbuk, Korea. Our results showed that the entire bacterial communities in the study sites include the phyla Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, which have been typically observed in forest soils. The composition ratio of Proteobacteria was the highest in the soil bacteria community. The results reflect that Proteobacteria is copiotroph, which generally favors relatively nutrient-rich conditions with abundant organic matter. Some rhizobia species such as Burkholderia, Bradyrhizobium, Rhizobium, which are known to contribute to soil nitrogen-fixation, exist in the study sites. As a result of correlation analysis between soil physicochemical characteristics and bacteria communities, the soil pH was significantly correlated with the soil bacteria compositions.

• Korean Journal of Environment and Ecology
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• v.35 no.5
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• pp.503-524
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• 2021

A largemouth bass (Micropterus salmoides) is an ecosystem disturbance fish species at the highest rank in the aquatic ecosystem, causing a serious imbalance in freshwater ecosystems. Although various attempts have been made to eradicate and control largemouth bass, no effective measures were found. Therefore, it is necessary to find an approach to maximize the effective population reduction based on the unique characteristics of largemouth bass. This study used the transcriptome analysis to derive 182,887 unigene contigs and select 12 types of final target sequences for applying the CRISPR/Cas9 system in the genes of IZUMO1 and Zona pellucida sperm-binding protein, which are proteins involved in sperm-egg recognition. After synthesizing 12 types of sgRNA capable of recognizing each target sequence, 12 types of Cas9-sgRNA ribonucleoprotein (RNP) complexes to be used in subsequent studies were prepared. This study searched the protein-coding gene of sperm-egg through the Next Generation Sequencing (NGS) and edited genes through the CRISPR/Cas9 system to induce infertile individuals that produced reproductive cells but could not form fertilized eggs. Through such a series of processes, it successfully established a composition development process for largemouth bass. It is judged that this study contributed to securing the valuable basic data for follow-up studies to verify its effect for the management of ecological disturbances without affecting the habitat of other endemic species in the same water system with the largemouth bass.

• Korean Journal of Clinical Laboratory Science
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• v.55 no.4
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• pp.235-243
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• 2023

As next-generation sequencing has been developed and used widely, RNA-sequencing (RNA-seq) has rapidly emerged as the first choice of tools to validate global transcriptome profiling. With the significant advances in RNA-seq, various types of RNA-seq have evolved in conjunction with the progress in bioinformatic tools. On the other hand, it is difficult to interpret the complex data underlying the biological meaning without a general understanding of the types of RNA-seq and bioinformatic approaches. In this regard, this paper discusses the two main sections of RNA-seq. First, two major variants of RNA-seq are described and compared with the standard RNA-seq. This provides insights into which RNA-seq method is most appropriate for their research. Second, the most widely used RNA-seq data analyses are discussed: (1) exploratory data analysis and (2) pathway enrichment analysis. This paper introduces the most widely used exploratory data analysis for RNA-seq, such as principal component analysis, heatmap, and volcano plot, which can provide the overall trends in the dataset. The pathway enrichment analysis section introduces three generations of pathway enrichment analysis and how they generate enriched pathways with the RNA-seq dataset.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.257-264
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• 2021

In this study, we analyzed the food components in the release product that sampled Sinonovacula constricta from the foreshore littoral at Byeongnyang-myeon, Suncheon Bay. We used microscopy and next-generation sequencing (NGS) to evaluate the applicability of morphological and molecular methods to analyze release products. The higher species diversity observed in the NGS method is due to the different levels of species identification, as microscopy displays morphological and anatomical levels of plankton species identification in S. constrita. Moreover, NGS can identify the level of species in the organic matter by using the 18s_V9 primer.